Align N-acetylglucosamine-specific PTS system, I, HPr, and IIA components (nagF) (characterized)
to candidate Dsui_0742 Dsui_0742 phosphoenolpyruvate-protein phosphotransferase
Query= reanno::BFirm:BPHYT_RS02740 (854 letters) >FitnessBrowser__PS:Dsui_0742 Length = 579 Score = 293 bits (749), Expect = 3e-83 Identities = 192/544 (35%), Positives = 289/544 (53%), Gaps = 17/544 (3%) Query: 292 TLAGVCAAPGVAVGKLVRWDDADIDPPEKANGTSAAESRLL--DKAIATVDADLDTTVRD 349 T+ G+ + G+A+G A ++ G A+ +L + AI V A+L+ + Sbjct: 4 TIHGLGVSGGIAIGVAQLMSHATLEVAHLTIGPRMADKEVLRFEAAILAVQAELEQLKLE 63 Query: 350 ASQRGAVGEAGIF-SVHRVLLEDPTLLDAARDLISLGK-SAGFAWREAIRAQIAILTNIE 407 AS+ A E F +H ++L DP L + + +I + +A +A + + +A I+ Sbjct: 64 ASKGNAPAELRAFVDLHGMILADPELSEVPKQIIRERRCNAEWAVVQQMERLVAQFDAID 123 Query: 408 DALLAERAADLRDIEKRVLRAL----GYTSATARTLPEEA---VLAAEEFTPSDLSTLDR 460 DA L ER AD+ + +RV++ L G ++ AR +E ++ A + +P+D Sbjct: 124 DAYLRERKADVVQVVERVVKVLMGHPGRSALRARKGGKETTDQIIVAHDLSPADTIGFKE 183 Query: 461 SRVTALVMARGGATSHAAILARQAGIPALVAVGDALHAIPEGTQVVVNATTGRLEFAPTE 520 R + + GGATSH AILAR IP++V + A I +G ++++ T G + P E Sbjct: 184 QRFASFITDVGGATSHTAILARSMAIPSIVGLHRARDLIRDGELLIIDGTRGVVIVNPDE 243 Query: 521 LDVERARLERTRLADVREANRRTSQQAAVTSDGRAIEVAANIATLDDAKTAVENGADSVG 580 +E RL ++ L R +R A T DG + + ANI +D + A GAD +G Sbjct: 244 RVLEEYRLRKSELELERSKLKRLKTMKATTLDGVDVLMYANIELPEDVEAARTAGADGIG 303 Query: 581 LLRTELLFIHRAAAPTTDEHRQSYQAIVDALSGRTAIIRTLDVGADKEVDYLTLPPEPNP 640 L RTE LF++R PT DE ++Y+ +V + G+ IRT D+GADK +D + + NP Sbjct: 304 LFRTEFLFLNRGDMPTEDEQFEAYRKVVKGMEGKPVTIRTFDLGADKALDAMD-RVKTNP 362 Query: 641 ALGLRGIRLAQVRPDLLDDQLRGLLAVQPLGAVRILLPMVTDVGEL---IRIRKRIDEFA 697 ALGLR IRL P + QLR +L G V+IL+PM+ E+ + + + Sbjct: 363 ALGLRAIRLQLAEPKMFRTQLRAILRASKYGKVKILIPMLAHAHEIDATLAAVQAAKQSL 422 Query: 698 RE--LGRTEPIEVGVMIEVPSAALLADQLAQHADFLSIGTNDLTQYTLAMDRCQADLAAQ 755 RE +G E IEVG MIE+P+AAL + DFLSIGTNDL QY LA+DR ++ Sbjct: 423 REQKIGFDEGIEVGGMIEIPAAALAIGMFLRRLDFLSIGTNDLIQYALAIDRSDETVSQL 482 Query: 756 ADGLHPAVLRLIAATVQGADKHGKWVGVCGALAGDPLAMPLLVGLGVTELSVDPVSVPGI 815 D LHPAVL L+A T+ +K G V VCG LAGDP LL+G+G+ S+ P + + Sbjct: 483 YDPLHPAVLMLVAHTIYSGEKAGLPVSVCGELAGDPAMTRLLLGMGLRVFSMHPSQILEV 542 Query: 816 KARV 819 K V Sbjct: 543 KQHV 546 Lambda K H 0.317 0.133 0.371 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 975 Number of extensions: 37 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 854 Length of database: 579 Length adjustment: 39 Effective length of query: 815 Effective length of database: 540 Effective search space: 440100 Effective search space used: 440100 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 54 (25.4 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory